Ttf1 (transcription termination factor 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ttf1 (transcription termination factor 1) Rattus norvegicus
Analyze
Symbol: Ttf1
Name: transcription termination factor 1
RGD ID: 1565673
Description: Predicted to enable DNA binding activity and chromatin binding activity. Predicted to be involved in termination of RNA polymerase I transcription. Predicted to act upstream of or within chromatin remodeling and transcription initiation at RNA polymerase I promoter. Predicted to be located in fibrillar center and nucleoplasm. Predicted to be active in nucleolus. Orthologous to human TTF1 (transcription termination factor 1); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH 6-propyl-2-thiouracil; all-trans-retinoic acid; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499766; RGD1565673; similar to RNA polymerase I transcription termination factor 1; transcription termination factor, RNA polymerase I
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,782,544 - 32,807,202 (+)NCBIGRCr8
mRatBN7.2312,384,626 - 12,409,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.037,635,630 - 7,660,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,984,215 - 13,008,867 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,067,017 - 8,086,185 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera37,163,853 - 7,188,383 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
fibrillar center  (ISO)
nucleolus  (IBA,ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. RNA polymerase I termination: Where is the end? Nemeth A, etal., Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):306-17. doi: 10.1016/j.bbagrm.2012.10.007. Epub 2012 Oct 23.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:7720715   PMID:9049305   PMID:19285000   PMID:22174936   PMID:22370158   PMID:29305861   PMID:33622350  


Genomics

Comparative Map Data
Ttf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,782,544 - 32,807,202 (+)NCBIGRCr8
mRatBN7.2312,384,626 - 12,409,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.037,635,630 - 7,660,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0312,984,215 - 13,008,867 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,067,017 - 8,086,185 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera37,163,853 - 7,188,383 (+)NCBICelera
Cytogenetic Map3p12NCBI
TTF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,375,548 - 132,406,840 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9132,375,548 - 132,406,851 (-)EnsemblGRCh38hg38GRCh38
GRCh379135,250,935 - 135,282,227 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,240,756 - 134,272,042 (-)NCBINCBI36Build 36hg18NCBI36
Build 349132,280,492 - 132,311,775NCBI
Celera9105,792,754 - 105,824,048 (-)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9104,744,257 - 104,775,555 (-)NCBIHuRef
CHM1_19135,400,954 - 135,432,252 (-)NCBICHM1_1
T2T-CHM13v2.09144,590,014 - 144,621,286 (-)NCBIT2T-CHM13v2.0
Ttf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,950,211 - 28,977,668 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl228,950,274 - 28,977,668 (+)EnsemblGRCm39 Ensembl
GRCm38229,060,199 - 29,087,656 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl229,060,262 - 29,087,656 (+)EnsemblGRCm38mm10GRCm38
MGSCv37228,915,783 - 28,943,170 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36228,882,286 - 28,909,115 (+)NCBIMGSCv36mm8
Celera228,766,271 - 28,793,645 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Ttf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555131,804,690 - 1,829,705 (-)NCBIChiLan1.0ChiLan1.0
TTF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,950,839 - 6,980,899 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan196,953,176 - 6,983,236 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09103,495,737 - 103,525,775 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,129,318 - 132,158,660 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,129,318 - 132,158,660 (-)Ensemblpanpan1.1panPan2
TTF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,855,565 - 51,881,000 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,855,559 - 51,878,459 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha951,120,246 - 51,145,642 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0952,748,649 - 52,774,067 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,746,666 - 52,772,199 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,528,526 - 51,553,908 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,852,982 - 51,876,680 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,939,290 - 51,964,688 (+)NCBIUU_Cfam_GSD_1.0
Ttf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,188,472 - 199,215,336 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648718,956,899 - 18,983,888 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648718,956,364 - 18,983,850 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,180,498 - 272,212,478 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,180,488 - 272,212,504 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,231,749 - 306,244,296 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TTF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,734,136 - 5,763,768 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,738,166 - 5,764,533 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660799,856,700 - 9,886,986 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ttf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247603,893,665 - 3,918,237 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ttf1
156 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:30
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000061029
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat

Markers in Region
BF406161  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2312,401,780 - 12,401,950 (+)MAPPERmRatBN7.2
Rnor_6.037,652,772 - 7,652,941NCBIRnor6.0
Rnor_5.0313,001,335 - 13,001,504UniSTSRnor5.0
RGSC_v3.438,079,996 - 8,080,165UniSTSRGSC3.4
Celera37,181,000 - 7,181,169UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 13 6 18 6 36 20 34 10
Low 43 44 35 1 35 8 11 38 15 7 1 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000061029   ⟹   ENSRNOP00000057745
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,385,040 - 12,409,257 (+)Ensembl
Rnor_6.0 Ensembl37,635,933 - 7,660,673 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099128   ⟹   ENSRNOP00000097927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,385,040 - 12,407,208 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113662   ⟹   ENSRNOP00000088164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,384,655 - 12,409,257 (+)Ensembl
RefSeq Acc Id: NM_001427196   ⟹   NP_001414125
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,647 - 32,807,198 (+)NCBI
RefSeq Acc Id: XM_006233882   ⟹   XP_006233944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,807,202 (+)NCBI
mRatBN7.2312,384,626 - 12,409,257 (+)NCBI
Rnor_6.037,635,630 - 7,660,153 (+)NCBI
Rnor_5.0312,984,215 - 13,008,867 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106155   ⟹   XP_038962083
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,791,932 (+)NCBI
mRatBN7.2312,384,626 - 12,393,976 (+)NCBI
RefSeq Acc Id: XM_039106156   ⟹   XP_038962084
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,789,503 (+)NCBI
mRatBN7.2312,384,626 - 12,391,558 (+)NCBI
RefSeq Acc Id: XM_063284344   ⟹   XP_063140414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,785,562 - 32,807,202 (+)NCBI
RefSeq Acc Id: XR_352207
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,782,544 - 32,801,357 (+)NCBI
mRatBN7.2312,384,626 - 12,406,749 (+)NCBI
Rnor_6.037,635,630 - 7,657,740 (+)NCBI
Rnor_5.0312,984,215 - 13,008,867 (+)NCBI
Sequence:
RefSeq Acc Id: XP_006233944   ⟸   XM_006233882
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B6I4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057745   ⟸   ENSRNOT00000061029
RefSeq Acc Id: XP_038962083   ⟸   XM_039106155
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038962084   ⟸   XM_039106156
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000088164   ⟸   ENSRNOT00000113662
RefSeq Acc Id: ENSRNOP00000097927   ⟸   ENSRNOT00000099128
RefSeq Acc Id: NP_001414125   ⟸   NM_001427196
- UniProtKB: A0A8I6B6I4 (UniProtKB/TrEMBL),   A6JTQ6 (UniProtKB/TrEMBL),   D4A1Z7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140414   ⟸   XM_063284344
- Peptide Label: isoform X2
Protein Domains
Myb-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A1Z7-F1-model_v2 AlphaFold D4A1Z7 1-857 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565673 AgrOrtholog
BioCyc Gene G2FUF-50264 BioCyc
Ensembl Genes ENSRNOG00000039777 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061029.5 UniProtKB/TrEMBL
  ENSRNOT00000099128.1 UniProtKB/TrEMBL
  ENSRNOT00000113662.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeodomain-like UniProtKB/TrEMBL
  SANT_DNA-bd UniProtKB/TrEMBL
NCBI Gene 499766 ENTREZGENE
PANTHER TRANSCRIPTION TERMINATION FACTOR 1 UniProtKB/TrEMBL
  TRANSCRIPTION TERMINATION FACTOR 1 UniProtKB/TrEMBL
Pfam Myb_DNA-bind_6 UniProtKB/TrEMBL
PhenoGen Ttf1 PhenoGen
PROSITE MYB_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039777 RatGTEx
SMART SANT UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A8I6AA77_RAT UniProtKB/TrEMBL
  A0A8I6B6I4 ENTREZGENE, UniProtKB/TrEMBL
  A6JTQ6 ENTREZGENE, UniProtKB/TrEMBL
  D4A1Z7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Ttf1  transcription termination factor 1  Ttf1  transcription termination factor, RNA polymerase I  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Ttf1  transcription termination factor, RNA polymerase I  RGD1565673_predicted  similar to RNA polymerase I transcription termination factor 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565673_predicted  similar to RNA polymerase I transcription termination factor 1 (predicted)  LOC499766  similar to RNA polymerase I transcription termination factor 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499766  similar to RNA polymerase I transcription termination factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL